There *might* be reasons to question evolution and other scientific theories; however this video is not one of them. It's taken from a television show "The Mysterious Origins of Man" produced by NBC in 1996. It simply repeats material from Cremo & Thompson's book 'Forbidden Archaeology', published in 1993. The 'evidence' presented in that book has been examined by many scholars. They universally rejected it: not to hide something, but because the book contains many mistakes, errors, poor arguments and misunderstanding. The authors, no matter what their viewpoint, simply don't have deep enough technical knowledge to describe or interpret their material accurately.
The television program was not a serious attempt to discuss archaeology: it was simply entertainment. Hence using Charlton Heston as presenter (a career low-point for an otherwise great actor). It was produced by NBC to make a profit, by getting people to watch television - nothing more. The History Channel is full of this stuff, shamefully.
There is no vast conspiracy by scientists - or by atheists - to suppress important information. Science doesn't proceed by looking for agreement; on the contrary, science works by critically evaluating evidence, and pointing out defects in arguments. 'Forbidden Archaeology' has been evaluated, and found to be nonsense from cover to cover.
Keep looking for critiques of science, if you want. Science thrives on critical thinking. There's nothing, absolutely nothing in this video to raise any doubts about modern science.
For details, see here:
http://www.talkorigins.org/faqs/mom.html
http://en.wikipedia.org/wiki/The_Mysterious_Origins_of_Man
http://ncse.com/rncse/28/1/mysterious-spheres-ottosdal-south-africa
http://chem.tufts.edu/science/franksteiger/nbcprog.htm
http://www.ucmp.berkeley.edu/fosrec/Lipps.html
Hope it helps.